Yes, you will need to manually create igroups and mapping on destination filer - they are not replicated. Also LUN serial numbers will change - this may be problem depending on host OS (e.g. VMware will not mount them by default).
I have done this before. Snapmirror the data, and the new controller will see the luns with "lun show". You're right, you'll need to configure the inititator groups, etc.
One caveat - luns have a serial number that I don't believe is copied with snapmirror. Some applications (Exchange comes to mind) are picky about this serial number; they won't let you use data on a different lun serial, even though it's the same drive letter. List the existing lun's serial with "lun serial <lun_path>", and set the new lun's serial with "lun serial <lun_path> <serial>".